Likely either could cause the error, but I would guess fsf. Peace,
Matt. From: -- <744652...@qq.com<mailto:744652...@qq.com>> Date: Saturday, April 29, 2017 at 6:46 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [SPAM] Re: [SPAM] Re: [SPAM] Re: [SPAM] Re: [HCP-Users][TaskfMRILevel2]feat_modelerror Thanks for your reply. Is this error due to missing fsf or EVs file? Then should I re-generate EVs and fsf? Best, Bai Haohao ------------------ Original ------------------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Sat, Apr 29, 2017 12:47 PM To: "--"<744652...@qq.com<mailto:744652...@qq.com>>; "hcp-users"<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>; Cc: "Brown, Tim"<tbbr...@wustl.edu<mailto:tbbr...@wustl.edu>>; Subject: Re: [SPAM] Re: [SPAM] Re: [SPAM] Re: [HCP-Users][TaskfMRILevel2]feat_modelerror I see: The fsf file is a part of the preprocessed fMRI packages together with the EVs. We should probably make a more descriptive error message for missing fsf or EVs. Peace, Matt. From: -- <744652...@qq.com<mailto:744652...@qq.com>> Date: Friday, April 28, 2017 at 10:51 PM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [SPAM] Re: [SPAM] Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_modelerror Thanks, here is the code that calls TaskfMRIAnalysis.sh in TaskfMRIAnalysisBatch.sh: ${queuing_command} ${HCPPIPEDIR}/TaskfMRIAnalysis/TaskfMRIAnalysis.sh \ --path=$StudyFolder \ --subject=$Subject \ --lvl1tasks=$LevelOneTasks \ --lvl1fsfs=$LevelOneFSFs \ --lvl2task=$LevelTwoTask \ --lvl2fsf=$LevelTwoFSF \ --lowresmesh=$LowResMesh \ --grayordinatesres=$GrayOrdinatesResolution \ --origsmoothingFWHM=$OriginalSmoothingFWHM \ --confound=$Confound \ --finalsmoothingFWHM=$FinalSmoothingFWHM \ --temporalfilter=$TemporalFilter \ --vba=$VolumeBasedProcessing # The following lines are used for interactive debugging to set the positional parameters: $1 $2 $3 ... echo "set -- --path=$StudyFolder \ --subject=$Subject \ --lvl1tasks=$LevelOneTasks \ --lvl1fsfs=$LevelOneFSFs \ --lvl2task=$LevelTwoTask \ --lvl2fsf=$LevelTwoFSF \ --lowresmesh=$LowResMesh \ --grayordinatesres=$GrayOrdinatesResolution \ --origsmoothingFWHM=$OriginalSmoothingFWHM \ --confound=$Confound \ --finalsmoothingFWHM=$FinalSmoothingFWHM \ --temporalfilter=$TemporalFilter \ --vba=$VolumeBasedProcessing" And the echo shows: set -- --path=/home/baihaohao/Workingdir/Data/HcpData --subject=100307 --lvl1tasks=tfMRI_EMOTION_RL@tfMRI_EMOTION_LR --lvl1fsfs=tfMRI_EMOTION_RL@tfMRI_EMOTION_LR --lvl2task=tfMRI_EMOTION --lvl2fsf=tfMRI_EMOTION --lowresmesh=32 --grayordinatesres=2 --origsmoothingFWHM=2 --confound=NONE --finalsmoothingFWHM=2 --temporalfilter=200 --vba=NO There is the code that calls TaskfMRILevel2.sh in TaskfMRIAnalysis.sh: echo "set -- $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing" ${PipelineScripts}/TaskfMRILevel2.sh $Subject $ResultsFolder $DownSampleFolder $LevelOnefMRINames $LevelOnefsfNames $LevelTwofMRIName $LevelTwofsfNames $LowResMesh $FinalSmoothingFWHM $TemporalFilter $VolumeBasedProcessing And the echo shows: set -- 100307 /home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/Results /home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/fsaverage_LR32k tfMRI_EMOTION_RL@tfMRI_EMOTION_LR tfMRI_EMOTION_RL@tfMRI_EMOTION_LR tfMRI_EMOTION tfMRI_EMOTION 32 2 200 NO And line56 of TaskfMRILevel2.sh is the red line here, which creates the error: #Make design files log_Msg "Make design files" DIR=`pwd` cd ${LevelTwoFEATDir} feat_model ${LevelTwoFEATDir}/design cd $DIR The path in ${LevelTwoFEATDir}: /home/baihaohao/Workingdir/Data/HcpData/100307/MNINonLinear/Results/tfMRI_EMOTION/tfMRI_EMOTION_hp200_s2_level2.feat Under the path, I can only found design.fsf, no design, even cp design.fsf design cannot fix this. Best, Bai Haohao ------------------ Original ------------------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Thu, Apr 27, 2017 09:59 PM To: "--"<744652...@qq.com<mailto:744652...@qq.com>>; "hcp-users"<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>; Subject: Re: [SPAM] Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_modelerror Perhaps you can paste in how you are calling the TaskfMRIAnalysis pipeline (not the run local part but rather what is in that script). Peace, Matt. From: -- <744652...@qq.com<mailto:744652...@qq.com>> Date: Thursday, April 27, 2017 at 8:48 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [SPAM] Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error The data and the Pipeline scripts are all included in the 2015 HCP Course, and the subject ID is 100307. Besides, I have already running three structural pipelines and two functional pipelines. Best, Bai Haohao ------------------ Original ------------------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Thu, Apr 27, 2017 09:08 PM To: "--"<744652...@qq.com<mailto:744652...@qq.com>>; "hcp-users"<hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>>; Subject: Re: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error Are you using HCP data or your own task fMRI data? Peace, Matt. From: -- <744652...@qq.com<mailto:744652...@qq.com>> Date: Thursday, April 27, 2017 at 3:56 AM To: Matt Glasser <glass...@wustl.edu<mailto:glass...@wustl.edu>>, hcp-users <hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>> Subject: [SPAM] Re: [HCP-Users] [TaskfMRILevel2]feat_model error Hello, I modify the TaskfMRIAnalysisBatch.sh to change StudyFolder, Subjlist and EnvironmentScript to my own file path. Then I write a bash file to call copy_evs_into_results.sh and generate_level1_fsf.sh to generate the files. Followed Day4_Practical7_Task_fMRI tutorial, I install level2.fsf file. After that, bash TaskfMRIAnalysisBatch.sh --runlocal Best, Bai Haohao ------------------ Original ------------------ From: "Glasser, Matthew";<glass...@wustl.edu<mailto:glass...@wustl.edu>>; Date: Wed, Apr 26, 2017 11:43 PM To: "--"<744652...@qq.com<mailto:744652...@qq.com>>; "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"<HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>>; Subject: Re: [HCP-Users] [TaskfMRILevel2]feat_model error How did you call the task analysis pipeline? Peace, Matt. From: <hcp-users-boun...@humanconnectome.org<mailto:hcp-users-boun...@humanconnectome.org>> on behalf of -- <744652...@qq.com<mailto:744652...@qq.com>> Date: Wednesday, April 26, 2017 at 10:35 AM To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>" <HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org>> Subject: [HCP-Users] [TaskfMRILevel2]feat_model error Hello HCP experts, I get a fatal error during running Examples/Scripts/TaskfMRIAnalysisBatch.sh, the error info(also see attached file): terminate called after throwing an instance of 'NEWMAT::ProgramException' /home/baihaohao/Workingdir/Pipelines-3.4.0/TaskfMRIAnalysis/scripts/TaskfMRILevel2.sh: line 56: 79213 Aborted (core dumped) feat_model ${LevelTwoFEATDir}/design and line56 of TaskfMRILevel2.sh is the red line here: #Make design files log_Msg "Make design files" DIR=`pwd` cd ${LevelTwoFEATDir} feat_model ${LevelTwoFEATDir}/design cd $DIR I have done steps based on HCP Course Materials Day4_Practical7_Task_fMRI tutorial, already install level1 and level2. How can I fix it? Any suggestion would be helpful. Thanks in advance, Bai Haohao _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org<mailto:HCP-Users@humanconnectome.org> http://lists.humanconnectome.org/mailman/listinfo/hcp-users ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. 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If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
